source: branches/lib/HELP_SOURCE/source/rna3d_dispBases.hlp

Last change on this file was 19532, checked in by westram, 4 months ago
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File size: 2.3 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      rna3d_general.hlp
5
6#       sub topics:
7#SUB     subtopic.hlp
8
9# format described in ../help.readme
10
11
12TITLE           Display options for the Residues/Bases
13
14OCCURRENCE      In ARB primary structure editor (ARB_EDIT4) -> RNA3D
15
16DESCRIPTION
17
18    To achieve more performance and dynamic overlay of any sequence associated
19    information, rendering (drawing) was simplified to chain display with the capacity to
20    display residues in the form nucleotides - Adenosine (A), Guanine (G), Cytosine (C)
21    and Uracil (U) at the respective coordinates in the molecule. Also viewing the entire
22    chemical structure in the molecule’s 3D structure is less readable.
23
24    Display Bases
25
26            By enabling the check box the corresponding residues in the rRNA sequence can
27            be displayed on the rRNA 3D structure. Disabling this check box will display
28            the molecule skeleton without residues.
29
30    Helix Region
31
32            Enabling this check box will display residues that are participating in Helix
33            formation in the secondary structure models of small subunit rRNA.
34
35    Unpaired Helix Region
36
37            Enabling this check box will display residues that are participating in bulge
38            (unpaired helix) formation in the secondary structure models of small subunit
39            rRNA.
40
41    Non-Helix Region
42
43            Enabling this check box will display residues that are participating in loop
44            (non-helix) formation in the secondary structure models of small subunit rRNA.
45
46    Display Size
47
48            The size of the residues displayed can be changed by specifying the desired
49            size in “Display size” box.
50
51    CHARACTERS
52
53            The corresponding residues are displayed with the actual nucleotides -
54            Adenosine (A), Guanine (G), Cytosine (C) and Uracil (U).
55
56    SHAPES
57
58            The corresponding residues are displayed with the respective shapes specified
59            for different structural motifs.
60
61    By setting different colors for the secondary structural motifs (loops, stems and
62    bulges) using “Color Settings”, the respective regions can be easily recognized in
63    the rRNA 3D structure.
64
65NOTES           None
66
67EXAMPLES        None
68
69WARNINGS        None
70
71BUGS            No bugs known
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